SGE Cluster Docking
SGE Cluster Information
- 'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.
- There are around 250 cluster nodes providing 600 total cores to run jobs in the sge queue as of May, 2009, named like 'node-1-1' through 'node-3-36' where the first number is the rack # and the second is the slot # in that rack.
- sgestat: high level overview of cluster status
- qsub: submit jobs
- qstat: check job status
- qdel: remove jobs
- qhost: check cluster status
- man sge_intro: start of manpage documentation
Typical Docking Workflow
- Generate spheres and grids - See Using MakeDOCK for more information, including how to prepare the receptor and ligand
ssh sgehead.compbio.ucsf.edu # ssh to SGE submit machine mkdir example # make docking directory cd example # change to docking directory cp <somedir>/rec.pdb . # copy or create rec.pdb cp <somedir>/xtal-lig.mol2 . # copy or create xtal-lig.mol2 (or even xtal-lig.pdb) startdockblaster5 # create spheres and grids # Check output for WARNING messages, correct as needed
- Setting up a docking run
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK md4db.csh bysubset 2 100 # create directories for docking run with 100 chunks # 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1) cd run.2 # chdir into run.2 directory
- Everything else
See MUD - Michael's Utilities for Docking for how to submit, check, and analyse the docking run.
For information on which ZINC